Variant report

Variant	rs11054433
Chromosome Location	chr12:11887446-11887447
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:11801538..11803993-chr12:11887220..11889492,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139083	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1009951	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1009953	0.85[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1009954	0.96[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10743967	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10845407	0.84[EUR][1000 genomes]
rs10845408	0.92[CEU][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes]
rs11054421	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs11054423	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs11054424	0.82[CEU][hapmap];0.91[EUR][1000 genomes]
rs11054429	0.93[EUR][1000 genomes]
rs11054439	0.89[CEU][hapmap];0.92[EUR][1000 genomes]
rs11615175	0.81[CEU][hapmap]
rs12228191	0.84[EUR][1000 genomes]
rs12369491	0.80[JPT][hapmap];0.85[EUR][1000 genomes]
rs17818461	0.85[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs17818498	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs17818624	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs2051525	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2187641	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs2187642	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2416882	0.83[EUR][1000 genomes]
rs2416883	0.81[EUR][1000 genomes]
rs2724588	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs2724616	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs2724618	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2724633	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs2724635	0.95[CHB][hapmap];0.91[ASN][1000 genomes]
rs2724645	0.86[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2724648	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs2856321	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs2856322	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2856324	0.86[CEU][hapmap];0.91[CHB][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2856344	0.86[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2860431	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs2900208	0.89[CEU][hapmap];0.90[JPT][hapmap];0.93[EUR][1000 genomes]
rs2954980	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs4763719	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4763720	0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs4763721	0.84[EUR][1000 genomes]
rs7488701	0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs762717	0.85[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs972798	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870039	chr12:11800363-11996598	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11873200-11902400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr12:11873200-11909400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:11873400-11894200	Weak transcription	NHLF	lung
4	chr12:11875000-11888600	Enhancers	Primary B cells from peripheral blood	blood
5	chr12:11878000-11888600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr12:11878000-11889600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr12:11880400-11896200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:11880600-11896400	Weak transcription	Fetal Stomach	stomach
9	chr12:11880800-11890800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr12:11882200-11888400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr12:11882400-11899200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr12:11882400-11902600	Weak transcription	Fetal Muscle Leg	muscle
13	chr12:11882400-11903200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr12:11883200-11894400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr12:11883600-11889600	Weak transcription	Fetal Kidney	kidney
16	chr12:11883600-11891400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr12:11883600-11891400	Weak transcription	Right Ventricle	heart
18	chr12:11883600-11894000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr12:11883600-11896200	Weak transcription	Colon Smooth Muscle	Colon
20	chr12:11883800-11906000	Weak transcription	Liver	Liver
21	chr12:11884000-11894000	Weak transcription	Right Atrium	heart
22	chr12:11884000-11894200	Weak transcription	Psoas Muscle	Psoas
23	chr12:11884200-11896200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr12:11884200-11899000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr12:11884800-11887800	Genic enhancers	Fetal Thymus	thymus
26	chr12:11884800-11893800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr12:11885000-11887800	Strong transcription	Dnd41	blood
28	chr12:11885000-11889600	Weak transcription	Spleen	Spleen
29	chr12:11885200-11889600	Weak transcription	Left Ventricle	heart
30	chr12:11885200-11890400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr12:11885200-11891400	Weak transcription	NHEK	skin
32	chr12:11885200-11891600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr12:11885200-11894200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr12:11885200-11894200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr12:11885200-11894200	Weak transcription	Osteobl	bone
36	chr12:11885200-11906200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:11885400-11891400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr12:11885600-11892000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr12:11885600-11894200	Weak transcription	Esophagus	oesophagus
40	chr12:11885600-11898600	Weak transcription	Primary T cells from cord blood	blood
41	chr12:11885600-11899000	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr12:11885600-11905200	Weak transcription	Fetal Intestine Large	intestine
43	chr12:11885800-11887600	Weak transcription	Duodenum Mucosa	Duodenum
44	chr12:11885800-11887600	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr12:11885800-11888200	Weak transcription	Pancreas	Pancrea
46	chr12:11885800-11889800	Weak transcription	Aorta	Aorta
47	chr12:11885800-11889800	Weak transcription	Lung	lung
48	chr12:11885800-11890600	Weak transcription	HUVEC	blood vessel
49	chr12:11885800-11893800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr12:11885800-11893800	Weak transcription	HMEC	breast

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